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    <title>MEME ChIP</title>
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    <h1><img src="http://meme.nbcr.net/meme/doc/images/memechip_logo.png" alt="MEME ChIP">
    </h1>
    <p>We process your sequences through a series of steps to help you identify motifs in your DNA sequences.</p>
    <p>
      If you use MEME-ChIP in your research, please cite the following paper:<br />
      <span class="citation">
        Philip Machanick and Timothy L. Bailey, "MEME-ChIP: motif analysis of large DNA datasets",
        <i>Bioinformatics</i>, <b>27</b>12, 1696-1697, 2011.
      </span>
    </p>
    <p>For more detail, see this <a href="http://meme.nbcr.net/meme/doc/meme-chip-tutorial.html">Tutorial</a>.
    You may find it helpful to open it in another window while examining your results.</p>
    
    
    

    

    
    
    <h2>Results</h2>
    <div style="padding-left:20px;">
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          <div style="padding-left:0em;">
          MEME output:
          
          
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="meme_out/meme.html">HTML</a> 
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="meme_out/meme.txt">plain text</a> 
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="meme_out/meme.xml">XML</a> 
          
        </td>
        
        <td >
          Motifs discovered in trimmed (central 100bp) input sequences.
        </td>
      </tr>
      
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        <td style="width: 15em; ">
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          TOMTOM output:
          
          
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="meme_tomtom_out/tomtom.html">HTML</a> 
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="meme_tomtom_out/tomtom.txt">plain text</a> 
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="meme_tomtom_out/tomtom.xml">XML</a> 
          
        </td>
        
        <td >
          Motifs from TranfacMatrix that match motifs MEME discovers.
        </td>
      </tr>
      
      <tr>
        <td style="width: 15em; ">
          <div style="padding-left:0em;">
          DREME output:
          
          
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="dreme_out/dreme.html">HTML</a> 
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="dreme_out/dreme.txt">plain text</a> 
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="dreme_out/dreme.xml">XML</a> 
          
        </td>
        
        <td >
          Motifs discovered in the trimmed (central 100bp) input sequences.
        </td>
      </tr>
      
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          <div style="padding-left:0em;">
          AME output:
          
          
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="ame_out/ame.html">HTML</a> 
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="ame_out/ame.txt">plain text</a> 
          
        </td>
        
        <td style="width: 10em;">
          
        </td>
        
        <td >
          Motif Enrichment Analysis of motifs from TranfacMatrix enriched in the trimmed (central 100bp) input sequences.
        </td>
      </tr>
      
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          CENTRIMO output:
          
          
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="centrimo_out/centrimo.html">HTML</a> 
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="centrimo_out/centrimo.txt">plain text</a> 
          
        </td>
        
        <td style="width: 10em;">
          
        </td>
        
        <td >
          Central Motif Enrichment Analysis of  MEME and DREME motifs in input sequences. The HTML results require a modern browser with full canvas support.
        </td>
      </tr>
      
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          SPAMO output:
          
          <br>(<a href="meme_spamo_out_stderr.txt">Warnings</a>)
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="meme_spamo_out/spamo.html">HTML</a> 
          
        </td>
        
        <td style="width: 10em;">
          
        </td>
        
        <td style="width: 10em;">
          
          <a href="meme_spamo_out/spamo.xml">XML</a> 
          
        </td>
        
        <td >
          Motif spacing analysis of 1st MEME motif to all other MEME and DREME motifs.
        </td>
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    <h2>Data</h2>
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          Input Sequences:
          
          
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="../SeqUnderPeaks.fa">SeqUnderPeaks.fa</a> 
          
        </td>
        
        <td style="width: 10em;">
          
        </td>
        
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        </td>
        
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          Your original untrimmed sequences.
        </td>
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          fasta-center output:
          
          
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="seqs-centered">seqs-centered</a> 
          
        </td>
        
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        </td>
        
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          Your sequences centered and trimed to width 100.
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          fasta-dinucleotide-shuffle output:
          
          
          </div>
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          <a href="seqs-shuffled">seqs-shuffled</a> 
          
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          The centered sequences randomly shuffled maintaining their dinucleotide frequency, used as a background for DREME and AME.
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          AME input:
          
          
          </div>
        </td>
        
        <td style="width: 10em;">
          
          <a href="seqs-centered_w_bg">seqs-centered_w_bg</a> 
          
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          The centered sequences followed by the same sequences after dinucleotide shuffling.
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    <h2>Commands</h2>
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mkdir /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs//Motif/MCF7/Denovo

fasta-center -len 100 &lt; /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/SeqUnderPeaks.fa &gt; /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-centered

fasta-dinucleotide-shuffle -f /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-centered -t -dinuc &gt; /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-shuffled

cat /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-centered /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-shuffled &gt; /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-centered_w_bg

meme /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-centered -oc /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/meme_out -dna -mod zoops -nmotifs 3 -minw 6 -maxw 30 -revcomp -nostatus

tomtom -verbosity 1 -oc /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 0.1 -no-ssc /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/meme_out/meme.txt /lustre/mib-cri/carrol09/Work/MyPipe/NewMeme/TranfacMatrix.meme

dreme -v 1 -oc /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/dreme_out -p /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-centered -n /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-shuffled -png

ame --verbose 1 --oc /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/ame_out --fix-partition 500 --bgformat 0 /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/seqs-centered_w_bg /lustre/mib-cri/carrol09/Work/MyPipe/NewMeme/TranfacMatrix.meme

centrimo -verbosity 1 -oc /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/centrimo_out /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/SeqUnderPeaks.fa /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/meme_out/meme.txt

spamo -verbosity 1 -oc /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/meme_spamo_out /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/SeqUnderPeaks.fa /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/meme_out/meme.txt /lustre/mib-cri/carrol09/Work/PipelinePracticeSet/Trial/20121114_MontoyaAR_DN_Hes6ChIP/Peaks/Macs/Motif/MCF7/Denovo/meme_out/meme.txt

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